Have you tried using hardware mode, with no speedhacks, and no graphical settings enabled, to see if the problem persists? For instance, try using native resolution, with no shadeboost, FXAA or FX Shaders enabled, and no anisotropic filtering on too or 8-bit textures. Use that as a baseline for testing. Try that baseline with speedhacks, if nothing broke, try enabling 8-bit textures, if that didn't break anything, try slowly increasing your resolution, though I would recommend using scaling instead of a custom res.